# Transcriptome analysis of 3D4/21 cells expressing CSFV NS4B

## TL;DR

This study uses RNA sequencing to explore how a viral protein from classical swine fever virus affects gene expression in pig cells, revealing impacts on processes like endocytosis, autophagy, and immune response.

## Contribution

The study identifies novel gene expression changes in cells expressing CSFV NS4B, linking NS4B to virus invasion, autophagy induction, and antiviral response inhibition.

## Key findings

- 4397 differentially expressed genes were identified in cells expressing CSFV NS4B compared to controls.
- NS4B regulates genes involved in endocytosis and intracellular trafficking, including CAV1/2, Rab1B, and VPS35.
- NS4B upregulates autophagy-related genes like WIPI2 and ATG16L2 while downregulating antiviral genes such as RIG-I and MDA5.

## Abstract

Classical swine fever (CSF) caused by classical swine fever virus (CSFV) has resulted in severe losses to the pig industry worldwide. CSFV non-structural protein 4B (NS4B) plays a crucial role in CSFV replication and pathogenicity. However, the function of NS4B is still limited during CSFV infection. In this study, the RNA-seq was used to investigate differentially expressed genes (DEGs) in 3D4/21 cells expressing CSFV NS4B. 4397 DEGs were identified in 3D4/21 cells expressing NS4B compared to cells expressing the empty vector (NC). Twelve DEGs were selected and further verified by RT-qPCR. Enrichment analyses of GO annotations and KEGG pathways revealed that these DEGs were associated with endocytosis, autophagy, cell adhesion, transport, immune response, apoptosis and so on. The expression of endocytosis-related genes, including CAV1/2, CAVIN2, Rab1B, CHMP2B/4C, VPS35, SNX2, Rab11B, CHMP6, MVB12B and VPS28, were found to be regulated. In addition, some genes associated with host immune defense, such as USP15, DHX29, DDX3, RIG-I and MDA5, were downregulated and the genes associated with host autophagy, such as WIPI2, ATG16L2, SMCR8, RPTOR and MLST8, were upregulated. Therefore, CSFV NS4B involved in virus invasion and intracellular trafficking, the induction of autophagy and the inhibition of antiviral response. Taken together, this study provides useful information for further understanding the function of NS4B during CSFV infection.